Progressive Cactus is a multiple-genome aligner for the thousand-genome era.
Progressive Cactus is a multiple-genome aligner for the thousand-genome era.
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DOI：
10.1038/s41586-020-2871-y
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发表时间：
2020-11
期刊：
影响因子：
64.8
通讯作者：
Paten B
中科院分区：
文献类型：
--
作者：
Armstrong J;Hickey G;Diekhans M;Fiddes IT;Novak AM;Deran A;Fang Q;Xie D;Feng S;Stiller J;Genereux D;Johnson J;Marinescu VD;Alföldi J;Harris RS;Lindblad-Toh K;Haussler D;Karlsson E;Jarvis ED;Zhang G;Paten B
由于测序成本的降低和第三代测序技术的改进，新的基因组组装正在以快速增长的速度到来。例如，NCBI（美国国家生物技术信息中心）数据库中的脊椎动物基因组组装数量在2018年7月至2019年7月的一年中增加了50%以上，达到1,485个组装。除了来自不同物种的组装体的涌入之外，还产生了新的人类从头组装体，这使得不仅能够分析小的多态性，而且能够分析人类个体和单倍型之间复杂的大规模结构差异。这个即将到来的时代及其前所未有的数据量为揭示基因组进化的许多见解提供了机会，但也提出了如何调整当前分析方法以满足规模增加的挑战。Cactus是一种无参考的多基因组比对程序，已被证明是高度准确的，但现有的实现随着基因组数量的增加而扩展性差，并且在高度重复序列的区域中挣扎。在这里，我们描述了Cactus的渐进扩展，以创建Progressive Cactus，它可以实现数十到数千个大型脊椎动物基因组的无参考比对，同时保持高比对质量。我们描述了600多个脊椎动物基因组的比对结果，据我们所知，这是迄今为止创建的最大的多脊椎动物基因组比对。Progressive Cactus程序可以有效地创建数百个大型脊椎动物基因组的无参考比对，并用于600多个脊椎动物基因组的比对。
New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far. The Progressive Cactus program can create reference-free alignments of hundreds of large vertebrate genomes efficiently, and is used for the alignment of more than 600 amniote genomes.
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影响因子：
5.8
作者：
Hickey, Glenn;Paten, Benedict;Haussler, David
通讯作者：
Haussler, David
影响因子：
64.8
作者：
Zoonomia Consortium
通讯作者：
Zoonomia Consortium
鸟类多样性的密集采样增强了比较基因组学的力量
影响因子：
64.8
作者：
Feng S;Stiller J;Deng Y;Armstrong J;Fang Q;Reeve AH;Xie D;Chen G;Guo C;Faircloth BC;Petersen B;Wang Z;Zhou Q;Diekhans M;Chen W;Andreu-Sánchez S;Margaryan A;Howard JT;Parent C;Pacheco G;Sinding MS;Puetz L;Cavill E;Ribeiro ÂM;Eckhart L;Fjeldså J;Hosner PA;Brumfield RT;Christidis L;Bertelsen MF;Sicheritz-Ponten T;Tietze DT;Robertson BC;Song G;Borgia G;Claramunt S;Lovette IJ;Cowen SJ;Njoroge P;Dumbacher JP;Ryder OA;Fuchs J;Bunce M;Burt DW;Cracraft J;Meng G;Hackett SJ;Ryan PG;Jønsson KA;Jamieson IG;da Fonseca RR;Braun EL;Houde P;Mirarab S;Suh A;Hansson B;Ponnikas S;Sigeman H;Stervander M;Frandsen PB;van der Zwan H;van der Sluis R;Visser C;Balakrishnan CN;Clark AG;Fitzpatrick JW;Bowman R;Chen N;Cloutier A;Sackton TB;Edwards SV;Foote DJ;Shakya SB;Sheldon FH;Vignal A;Soares AER;Shapiro B;González-Solís J;Ferrer-Obiol J;Rozas J;Riutort M;Tigano A;Friesen V;Dalén L;Urrutia AO;Székely T;Liu Y;Campana MG;Corvelo A;Fleischer RC;Rutherford KM;Gemmell NJ;Dussex N;Mouritsen H;Thiele N;Delmore K;Liedvogel M;Franke A;Hoeppner MP;Krone O;Fudickar AM;Milá B;Ketterson ED;Fidler AE;Friis G;Parody-Merino ÁM;Battley PF;Cox MP;Lima NCB;Prosdocimi F;Parchman TL;Schlinger BA;Loiselle BA;Blake JG;Lim HC;Day LB;Fuxjager MJ;Baldwin MW;Braun MJ;Wirthlin M;Dikow RB;Ryder TB;Camenisch G;Keller LF;DaCosta JM;Hauber ME;Louder MIM;Witt CC;McGuire JA;Mudge J;Megna LC;Carling MD;Wang B;Taylor SA;Del-Rio G;Aleixo A;Vasconcelos ATR;Mello CV;Weir JT;Haussler D;Li Q;Yang H;Wang J;Lei F;Rahbek C;Gilbert MTP;Graves GR;Jarvis ED;Paten B;Zhang G
通讯作者：
Zhang G
DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G
影响因子：
14.9
作者：
Frankish A;Diekhans M;Ferreira AM;Johnson R;Jungreis I;Loveland J;Mudge JM;Sisu C;Wright J;Armstrong J;Barnes I;Berry A;Bignell A;Carbonell Sala S;Chrast J;Cunningham F;Di Domenico T;Donaldson S;Fiddes IT;García Girón C;Gonzalez JM;Grego T;Hardy M;Hourlier T;Hunt T;Izuogu OG;Lagarde J;Martin FJ;Martínez L;Mohanan S;Muir P;Navarro FCP;Parker A;Pei B;Pozo F;Ruffier M;Schmitt BM;Stapleton E;Suner MM;Sycheva I;Uszczynska-Ratajczak B;Xu J;Yates A;Zerbino D;Zhang Y;Aken B;Choudhary JS;Gerstein M;Guigó R;Hubbard TJP;Kellis M;Paten B;Reymond A;Tress ML;Flicek P
通讯作者：
Flicek P